See the script phase documentation for details, especially the “Specify the Input and Output Files for Your Script” section. You need to edit your build phase and specify which files your script is using as input (if any) and which files it’s going to generate.
Using this information, the Xcode build process can determine whether a script phase needs to be run: if the input files haven’t changed, there’s no need to run the script phase at all. If it does run, Xcode at least knows which output files were generated and thus which other build processes depending on these files need to be run.
See also the “Declare Inputs and Outputs for Custom Scripts and Build Rules” section in Improving the Speed of Incremental Builds